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        Module&nbsp;ijtools
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ijtools</h1><p class="nomargin-top"><span class="codelink"><a href="ijtools-pysrc.html">source&nbsp;code</a></span></p>
<p>Interface to ImageJ API, making functions more 'Pythonic'</p>

<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Functions</span></td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">ImagePlus</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="getImage"></a><span class="summary-sig-name">getImage</span>()</span><br />
      Returns a reference to the active image.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getImage">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">list of lists of ints</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getPixels" class="summary-sig-name">getPixels</a>(<span class="summary-sig-arg">slice</span>=<span class="summary-sig-default">None</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Returns the pixels of the given ImageJ as a python 2D list.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getPixels">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#setPixels" class="summary-sig-name">setPixels</a>(<span class="summary-sig-arg">pixels</span>,
        <span class="summary-sig-arg">slice</span>=<span class="summary-sig-default">None</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Sets the given 2D pixel list into the image.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#setPixels">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">int or str</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getBitDepth" class="summary-sig-name">getBitDepth</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>,
        <span class="summary-sig-arg">numpy</span>=<span class="summary-sig-default">False</span>)</span><br />
      Returns the bit depth of the given image.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getBitDepth">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">int</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#nSlices" class="summary-sig-name">nSlices</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Returns the number of slices on the image.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#nSlices">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#setSlice" class="summary-sig-name">setSlice</a>(<span class="summary-sig-arg">n</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Sets the selected slice to 'n'.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#setSlice">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">(int, int, int)</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getShape" class="summary-sig-name">getShape</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Return the image shape as a tuple of (nslices, width, height).</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getShape">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#showMessage" class="summary-sig-name">showMessage</a>(<span class="summary-sig-arg">msg</span>,
        <span class="summary-sig-arg">title</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
      Displays a message in a dialog box titled &quot;Message&quot;.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#showMessage">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#showStatus" class="summary-sig-name">showStatus</a>(<span class="summary-sig-arg">msg</span>)</span><br />
      Displays a message in the ImageJ status bar.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#showStatus">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#showProgress" class="summary-sig-name">showProgress</a>(<span class="summary-sig-arg">index</span>,
        <span class="summary-sig-arg">finalIndex</span>=<span class="summary-sig-default">None</span>)</span><br />
      Shows the progress bar in the ImageJ window:</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#showProgress">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getString" class="summary-sig-name">getString</a>(<span class="summary-sig-arg">prompt</span>,
        <span class="summary-sig-arg">defaultString</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
      Allows the user to enter a string in a dialog box.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getString">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getNumber" class="summary-sig-name">getNumber</a>(<span class="summary-sig-arg">prompt</span>,
        <span class="summary-sig-arg">defaultValue</span>=<span class="summary-sig-default">0</span>)</span><br />
      Allows the user to enter a string in a dialog box.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getNumber">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">str</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getPrefs" class="summary-sig-name">getPrefs</a>(<span class="summary-sig-arg">key</span>,
        <span class="summary-sig-arg">default</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
      Uses the keyword key to retrieve a string from the preferences file.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getPrefs">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#setPrefs" class="summary-sig-name">setPrefs</a>(<span class="summary-sig-arg">key</span>,
        <span class="summary-sig-arg">value</span>)</span><br />
      Saves value in the preferences file using the keyword key.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#setPrefs">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">str</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getTitle" class="summary-sig-name">getTitle</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Returns the image name.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getTitle">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#run" class="summary-sig-name">run</a>(<span class="summary-sig-arg">command</span>,
        <span class="summary-sig-arg">options</span>=<span class="summary-sig-default">None</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Runs an ImageJ command using the specified image and options.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#run">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#close" class="summary-sig-name">close</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Closes the image and sets the pixel arrays to null.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#close">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#updateAndDraw" class="summary-sig-name">updateAndDraw</a>(<span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Updates the image from the pixel data in its associated 
      ImageProcessor, then displays it.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#updateAndDraw">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#error" class="summary-sig-name">error</a>(<span class="summary-sig-arg">msg</span>,
        <span class="summary-sig-arg">title</span>=<span class="summary-sig-default">None</span>)</span><br />
      Displays a message in a dialog box with the specified title.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#error">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">str</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#getDirectory" class="summary-sig-name">getDirectory</a>(<span class="summary-sig-arg">title</span>)</span><br />
      Returns the path to the home (&quot;user.home&quot;), startup (ImageJ
      directory), plugins, macros, temp, current or image directory if 
      title is &quot;home&quot;, &quot;startup&quot;, &quot;plugins&quot;, 
      &quot;macros&quot;, &quot;temp&quot;, &quot;current&quot; or 
      &quot;image&quot;, otherwise, displays a dialog and returns the path 
      to the directory selected by the user.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#getDirectory">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#openBrowser" class="summary-sig-name">openBrowser</a>(<span class="summary-sig-arg">url</span>)</span><br />
      Attempts to open the default web browser to the given URL.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#openBrowser">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#setTitle" class="summary-sig-name">setTitle</a>(<span class="summary-sig-arg">title</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Sets the image name.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#setTitle">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">bool</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="isWindows"></a><span class="summary-sig-name">isWindows</span>()</span><br />
      Returns true if this machine is running Windows.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#isWindows">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">bool</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="isVista"></a><span class="summary-sig-name">isVista</span>()</span><br />
      Returns true if ImageJ is running on Windows Vista.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#isVista">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">None</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="ijtools-module.html#rename" class="summary-sig-name">rename</a>(<span class="summary-sig-arg">title</span>,
        <span class="summary-sig-arg">im</span>=<span class="summary-sig-default">None</span>)</span><br />
      Sets the image name.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="ijtools-pysrc.html#setTitle">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Variables</span></td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="__package__"></a><span class="summary-name">__package__</span> = <code title="None">None</code>
    </td>
  </tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Function Details</span></td>
</tr>
</table>
<a name="getPixels"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getPixels</span>(<span class="sig-arg">slice</span>=<span class="sig-default">None</span>,
        <span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getPixels">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Returns the pixels of the given ImageJ as a python 2D list.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>slice</code></strong> (int or None) - get pixels from the specified slice number, if 'None' use current
          selected slice.</li>
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: list of lists of ints</dt>
        <dd>python 2D list of ints</dd>
  </dl>
</td></tr></table>
</div>
<a name="setPixels"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">setPixels</span>(<span class="sig-arg">pixels</span>,
        <span class="sig-arg">slice</span>=<span class="sig-default">None</span>,
        <span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#setPixels">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Sets the given 2D pixel list into the image.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>pixels</code></strong> (list of lists of ints) - python 2D list of ints</li>
        <li><strong class="pname"><code>slice</code></strong> (int or None) - set pixels on the specified slice number, if 'None' use current</li>
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getBitDepth"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getBitDepth</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>,
        <span class="sig-arg">numpy</span>=<span class="sig-default">False</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getBitDepth">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Returns the bit depth of the given image.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
        <li><strong class="pname"><code>numpy</code></strong> (bool) - if true, return bit depth on Numpy dtype compatible format.</li>
    </ul></dd>
    <dt>Returns: int or str</dt>
  </dl>
</td></tr></table>
</div>
<a name="nSlices"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">nSlices</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#nSlices">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Returns the number of slices on the image.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: int</dt>
  </dl>
</td></tr></table>
</div>
<a name="setSlice"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">setSlice</span>(<span class="sig-arg">n</span>,
        <span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#setSlice">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Sets the selected slice to 'n'.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
        <li><strong class="pname"><code>n</code></strong> (int)</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getShape"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getShape</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getShape">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Return the image shape as a tuple of (nslices, width, height).</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: (int, int, int)</dt>
  </dl>
</td></tr></table>
</div>
<a name="showMessage"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">showMessage</span>(<span class="sig-arg">msg</span>,
        <span class="sig-arg">title</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#showMessage">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Displays a message in a dialog box titled &quot;Message&quot;.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>msg</code></strong> (str) - text to be shown</li>
        <li><strong class="pname"><code>title</code></strong> (str) - dialog box title</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="showStatus"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">showStatus</span>(<span class="sig-arg">msg</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#showStatus">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Displays a message in the ImageJ status bar.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>msg</code></strong> (str) - text to be shown</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="showProgress"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">showProgress</span>(<span class="sig-arg">index</span>,
        <span class="sig-arg">finalIndex</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#showProgress">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Shows the progress bar in the ImageJ window:</p>
  <p>If finalIndex==None -&gt; Updates the progress bar, where 
  0&lt;=progress&lt;=1.0. If finalIndex!=None -&gt; Updates the progress 
  bar, where the length of the bar is set to (currentValue+1)/finalValue of
  the maximum bar length.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>index</code></strong> (number)</li>
        <li><strong class="pname"><code>finalIndex</code></strong> (int)</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getString"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getString</span>(<span class="sig-arg">prompt</span>,
        <span class="sig-arg">defaultString</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getString">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Allows the user to enter a string in a dialog box.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>prompt</code></strong> (str)</li>
        <li><strong class="pname"><code>defaultString</code></strong> (str)</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getNumber"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getNumber</span>(<span class="sig-arg">prompt</span>,
        <span class="sig-arg">defaultValue</span>=<span class="sig-default">0</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getNumber">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Allows the user to enter a string in a dialog box.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>defaultValue</code></strong> (number)</li>
        <li><strong class="pname"><code>prompt</code></strong> (str)</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getPrefs"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getPrefs</span>(<span class="sig-arg">key</span>,
        <span class="sig-arg">default</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getPrefs">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Uses the keyword key to retrieve a string from the preferences 
  file.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>key</code></strong> (str) - keyword associated to the preference</li>
        <li><strong class="pname"><code>default</code></strong> (str) - default value of the preference</li>
    </ul></dd>
    <dt>Returns: str</dt>
        <dd>preference</dd>
  </dl>
</td></tr></table>
</div>
<a name="setPrefs"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">setPrefs</span>(<span class="sig-arg">key</span>,
        <span class="sig-arg">value</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#setPrefs">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Saves value in the preferences file using the keyword key.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>key</code></strong> (str) - keyword associated to the preference</li>
        <li><strong class="pname"><code>value</code></strong> (str) - value to store in the preferences</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getTitle"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getTitle</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getTitle">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Returns the image name.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: str</dt>
        <dd>image name</dd>
  </dl>
</td></tr></table>
</div>
<a name="run"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">run</span>(<span class="sig-arg">command</span>,
        <span class="sig-arg">options</span>=<span class="sig-default">None</span>,
        <span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#run">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Runs an ImageJ command using the specified image and options.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
        <li><strong class="pname"><code>command</code></strong> (str)</li>
        <li><strong class="pname"><code>options</code></strong> (str)</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="close"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">close</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#close">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Closes the image and sets the pixel arrays to null.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="updateAndDraw"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">updateAndDraw</span>(<span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#updateAndDraw">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Updates the image from the pixel data in its associated 
  ImageProcessor, then displays it.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="error"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">error</span>(<span class="sig-arg">msg</span>,
        <span class="sig-arg">title</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#error">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Displays a message in a dialog box with the specified title.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>msg</code></strong> (str) - message to be displayed</li>
        <li><strong class="pname"><code>title</code></strong> (str) - dialog box title</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="getDirectory"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">getDirectory</span>(<span class="sig-arg">title</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#getDirectory">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Returns the path to the home (&quot;user.home&quot;), startup (ImageJ 
  directory), plugins, macros, temp, current or image directory if title is
  &quot;home&quot;, &quot;startup&quot;, &quot;plugins&quot;, 
  &quot;macros&quot;, &quot;temp&quot;, &quot;current&quot; or 
  &quot;image&quot;, otherwise, displays a dialog and returns the path to 
  the directory selected by the user.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>title</code></strong> (str)</li>
    </ul></dd>
    <dt>Returns: str</dt>
  </dl>
</td></tr></table>
</div>
<a name="openBrowser"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">openBrowser</span>(<span class="sig-arg">url</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#openBrowser">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Attempts to open the default web browser to the given URL.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>url</code></strong> (str) - url to open</li>
    </ul></dd>
    <dt>Returns: None</dt>
  </dl>
</td></tr></table>
</div>
<a name="setTitle"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">setTitle</span>(<span class="sig-arg">title</span>,
        <span class="sig-arg">im</span>=<span class="sig-default">None</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="ijtools-pysrc.html#setTitle">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Sets the image name.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>title</code></strong> (str) - image title to be set</li>
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
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  <h3 class="epydoc"><span class="sig"><span class="sig-name">rename</span>(<span class="sig-arg">title</span>,
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    ><span class="codelink"><a href="ijtools-pysrc.html#setTitle">source&nbsp;code</a></span>&nbsp;
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  <p>Sets the image name.</p>
  <dl class="fields">
    <dt>Parameters:</dt>
    <dd><ul class="nomargin-top">
        <li><strong class="pname"><code>title</code></strong> (str) - image title to be set</li>
        <li><strong class="pname"><code>im</code></strong> (ImageJ ImagePlus) - ImageJ ImagePlus to use, if 'None' use the current select image.</li>
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